[Bioperl-l] Ask help for Bio::Tools::Run::Primer3

[Brian Osborne]

Jason,

And, as you know, one can also do:

  my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>$seq,
                                              -outfile=>"temp.out",
                                              -path=>"/usr/bin/primer3_core"
);

Tested in Cygwin, not Windows.

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jason Stajich
Sent: Friday, October 01, 2004 10:01 AM
To: Bioperl Mailing List
Subject: Re: [Bioperl-l] Ask help for Bio::Tools::Run::Primer3

In looking at the code some more, shouldn't we make the default
'primer3_core' instead?

You can always override it with the program_name function.
$primer3->program_name('my_superfast_primer3');

-jason
On Sep 29, 2004, at 4:38 PM, Ewing, Adam D. wrote:

> Yes, it does matter... simply change the name of primer3_core to
> primer3, put it in your path, and you should be good to go!
>
> Adam
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org on behalf of Fengkai Zhang
> (Tony)
> Sent: Wed 9/29/2004 4:21 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Ask help for Bio::Tools::Run::Primer3
>
> Hi, I am a newbie for bioperl and met the below question.
>
> I was trying to use Bio::Tools::Run::Primer3. When I run the example
> code in the documentation of this module, I got the following error
> message:
> --------------------------------
> <shell> $ perl -I ../primer3_1.0.0/src/ -w primer3run_test.pl
>
> Use of uninitialized value in concatenation (.) or string at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Primer3.pm line 212,
> <GEN0> line 1.
> primer3 can not be found. Is it installed?
> --------------------------------
>
> I already installed Primer3 according its instruction and it works
> well to run the test and example. I also noticed that the
> primer_test.pl in primer3 package calls "primer3_core" rather than
> "primer3". Does it matter for Bio::Tools::Run::Primer3 module?
>
>
> Thanks ahead for your help.
>
>
>
> Tony
>
> VIPBG at VCU
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

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